{"action":"opened","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/2395","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2395/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2395/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2395/events","html_url":"https://github.com/broadinstitute/gatk/issues/2395","id":206004724,"number":2395,"title":"SamAssertionUtils.samsEqualStringent reverts to read by read comparison often","user":{"login":"cmnbroad","id":10062863,"avatar_url":"https://avatars.githubusercontent.com/u/10062863?v=3","gravatar_id":"","url":"https://api.github.com/users/cmnbroad","html_url":"https://github.com/cmnbroad","followers_url":"https://api.github.com/users/cmnbroad/followers","following_url":"https://api.github.com/users/cmnbroad/following{/other_user}","gists_url":"https://api.github.com/users/cmnbroad/gists{/gist_id}","starred_url":"https://api.github.com/users/cmnbroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmnbroad/subscriptions","organizations_url":"https://api.github.com/users/cmnbroad/orgs","repos_url":"https://api.github.com/users/cmnbroad/repos","events_url":"https://api.github.com/users/cmnbroad/events{/privacy}","received_events_url":"https://api.github.com/users/cmnbroad/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-02-07T20:27:45Z","updated_at":"2017-02-07T20:27:45Z","closed_at":null,"body":"SamAssertionUtils.samsEqualStringent tries to short-circuit file validation by first doing an md5 compare. Most of the time when we run the test suite (in the current tests 171 out of 193), the short-circuiting fails we do the more expensive read by read test.\r\n\r\nAll of these have one or more that fail md5 check (some are probably crams, which IIRC places the file name in the cram header):\r\n\r\nMarkDuplicatesIntegrationTest\r\nAddOrReplaceReadGroupsIntegrationTest\r\nApplyBQSRIntegrationTest\r\nApplyBQSRSparkIntegrationTest\r\nBQSRPipelineSparkIntegrationTest\r\nBwaSparkIntegrationTest\r\nGatherBamFilesIntegrationTest\r\nHaplotypeBAMWriterUnitTest\r\nPrintReadsIntegrationTest\r\nReadsPipelineSparkIntegrationTest\r\nSamAssertionUtilsUnitTest\r\nSamFormatConverterIntegrationTest\r\nSortReadFileSparkIntegrationTest\r\nSortSamIntegrationTest\r\nSplitNCigarReadsIntegrationTest\r\nClipReadsIntegrationTest\r\n"}}
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